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Yorodumi- PDB-4aq0: Structure of the Gh92 Family Glycosyl Hydrolase Ccman5 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aq0 | ||||||
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Title | Structure of the Gh92 Family Glycosyl Hydrolase Ccman5 in complex with deoxymannojirimycin | ||||||
Components | CCMAN5 | ||||||
Keywords | HYDROLASE / MANNOSIDASE | ||||||
Function / homology | Function and homology information alpha-mannosidase / alpha-mannosidase activity / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | CELLULOSIMICROBIUM CELLULANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Baranova, E. / Tiels, P. / Callewaert, N. / Remaut, H. | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2012 Title: A Bacterial Glycosidase Enables Mannose-6-Phosphate Modification and Improved Cellular Uptake of Yeast-Produced Recombinant Human Lysosomal Enzymes. Authors: Tiels, P. / Baranova, E. / Piens, K. / De Visscher, C. / Pynaert, G. / Nerinckx, W. / Stout, J. / Fudalej, F. / Hulpiau, P. / Tannler, S. / Geysens, S. / Van Hecke, A. / Valevska, A. / ...Authors: Tiels, P. / Baranova, E. / Piens, K. / De Visscher, C. / Pynaert, G. / Nerinckx, W. / Stout, J. / Fudalej, F. / Hulpiau, P. / Tannler, S. / Geysens, S. / Van Hecke, A. / Valevska, A. / Vervecken, W. / Remaut, H. / Callewaert, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aq0.cif.gz | 313.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aq0.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 4aq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aq0_validation.pdf.gz | 744.1 KB | Display | wwPDB validaton report |
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Full document | 4aq0_full_validation.pdf.gz | 746 KB | Display | |
Data in XML | 4aq0_validation.xml.gz | 58.7 KB | Display | |
Data in CIF | 4aq0_validation.cif.gz | 88.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/4aq0 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aq0 | HTTPS FTP |
-Related structure data
Related structure data | 2xsgSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 84292.852 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-774 Source method: isolated from a genetically manipulated source Details: N-TERMINAL FRAGMENT CORRESPONDING TO CATALYTIC DOMAIN. Source: (gene. exp.) CELLULOSIMICROBIUM CELLULANS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1E1E9*PLUS, alpha-mannosidase #2: Chemical | #3: Chemical | ChemComp-B3P / | #4: Chemical | ChemComp-DMJ / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.69 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M NA FLUORIDE, 0.1 M BIS TRIS PROPANE PH 7.5 AND 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0725 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0725 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→55.5 Å / Num. obs: 95933 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XSG Resolution: 2.09→55.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.764 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.283 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→55.5 Å
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Refine LS restraints |
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